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Genome-wide association study

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https://www.readbyqxmd.com/read/29228370/a-nf-%C3%AE%C2%BAb-signature-predicts-low-grade-glioma-prognosis-a-precision-medicine-approach-based-on-patient-derived-stem-cells
#1
Tamara Ius, Yari Ciani, Maria Elisabetta Ruaro, Miriam Isola, Marisa Sorrentino, Michela Bulfoni, Veronica Candotti, Cecilia Correcig, Evgenia Bourkoula, Ivana Manini, Enrico Pegolo, Damiano Mangoni, Stefania Marzinotto, Slobodanka Radovic, Barbara Toffoletto, Federica Caponnetto, Andrea Zanello, Laura Mariuzzi, Carla Di Loreto, Antonio Paolo Beltrami, Silvano Piazza, Miran Skrap, Daniela Cesselli
Background: While recent genome wide association studies have suggested novel low-grade glioma (LGG) stratification models based on a molecular classification, we explored the potential clinical utility of patient-derived cells. Specifically, we assayed glioma-associated stem cells (GASC) that are patient-derived stem cells representative of the glioma microenvironment. Methods: By next generation sequencing, we analyzed the transcriptional profile of GASC derived from patients that underwent anaplastic transformation either within 48 months (GASC-BAD) or ≥7 years (GASC-GOOD) after surgery...
December 7, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29228366/genotype-influences-day-to-day-variability-in-sleep-in-drosophila-melanogaster
#2
Katherine J Wu, Shailesh Kumar, Yazmin L Serrano Negron, Susan T Harbison
Patterns of sleep often vary among individuals. But sleep and activity may also vary within an individual, fluctuating in pattern across time. One possibility is that these daily fluctuations in sleep are caused by the underlying genotype of the individual. However, differences attributable to genetic causes are difficult to distinguish from environmental factors in outbred populations such as humans. We therefore employed Drosophila as a model of intra-individual variability in sleep using previously collected sleep and activity data from the Drosophila Genetic Reference Panel, a collection of wild-derived inbred lines...
December 8, 2017: Sleep
https://www.readbyqxmd.com/read/29228058/altered-intragenic-dna-methylation-of-hook2-gene-in-adipose-tissue-from-individuals-with-obesity-and-type-2-diabetes
#3
Sandra Rodríguez-Rodero, Edelmiro Menéndez-Torre, Gustavo Fernández-Bayón, Paula Morales-Sánchez, Lourdes Sanz, Estrella Turienzo, Juan José González, Ceferino Martinez-Faedo, Lorena Suarez-Gutiérrez, Jessica Ares, Lucia Díaz-Naya, Alicia Martin-Nieto, Juan L Fernández-Morera, Mario F Fraga, Elías Delgado-Álvarez
AIMS/HYPOTHESIS: Failure in glucose response to insulin is a common pathology associated with obesity. In this study, we analyzed the genome wide DNA methylation profile of visceral adipose tissue (VAT) samples in a population of individuals with obesity and assessed whether differential methylation profiles are associated with the presence of type 2 diabetes (T2D). METHODS: More than 485,000 CpG genome sites from VAT samples from women with obesity undergoing gastric bypass (n = 18), and classified as suffering from type 2 diabetes (T2D) or not (no type 2 diabetes, NT2D), were analyzed using DNA methylation arrays...
2017: PloS One
https://www.readbyqxmd.com/read/29228046/genome-wide-microarray-analysis-leads-to-identification-of-genes-in-response-to-herbicide-metribuzin-in-wheat-leaves
#4
Whitney Pilcher, Hana Zandkamiri, Kelly Arceneaux, Stephen Harrison, Niranjan Baisakh
Herbicides are an important component of weed management in wheat, particularly in the southeastern US where weeds actively compete with wheat throughout the winter for nutrients and reduce tillering and ultimately the yield of the crop. Some wheat varieties are sensitive to metribuzin, a low-cost non-selective herbicide, leading to leaf chlorosis, stand loss, and decreased yield. Knowledge of the genetics of herbicide tolerance in wheat is very limited and most new varieties have not been screened for metribuzin tolerance...
2017: PloS One
https://www.readbyqxmd.com/read/29228018/genome-wide-association-study-identifies-a-locus-associated-with-rotator-cuff-injury
#5
Thomas R Roos, Andrew K Roos, Andrew L Avins, Marwa A Ahmed, John P Kleimeyer, Michael Fredericson, John P A Ioannidis, Jason L Dragoo, Stuart K Kim
Rotator cuff tears are common, especially in the fifth and sixth decades of life, but can also occur in the competitive athlete. Genetic differences may contribute to overall injury risk. Identifying genetic loci associated with rotator cuff injury could shed light on the etiology of this injury. We performed a genome-wide association screen using publically available data from the Research Program in Genes, Environment and Health including 8,357 cases of rotator cuff injury and 94,622 controls. We found rs71404070 to show a genome-wide significant association with rotator cuff injury with p = 2...
2017: PloS One
https://www.readbyqxmd.com/read/29227965/human-longevity-25-genetic-loci-associated-in-389-166-uk-biobank-participants
#6
Luke C Pilling, Chia-Ling Kuo, Kamil Sicinski, Jone Tamosauskaite, George A Kuchel, Lorna W Harries, Pamela Herd, Robert Wallace, Luigi Ferrucci, David Melzer
We undertook a genome-wide association study (GWAS) of parental longevity in European descent UK Biobank participants. For combined mothers' and fathers' attained age, 10 loci were associated (p<5*10-8), including 8 previously identified for traits including survival, Alzheimer's and cardiovascular disease. Of these, 4 were also associated with longest 10% survival (mothers age ≥90 years, fathers ≥87 years), with 2 additional associations including MC2R intronic variants (coding for the adrenocorticotropic hormone receptor)...
December 6, 2017: Aging
https://www.readbyqxmd.com/read/29226559/nature-s-genetic-screens-using-genome-wide-association-studies-for-effector-discovery
#7
Andrea Sánchez-Vallet, Fanny E Hartmann, Thierry C Marcel, Daniel Croll
No abstract text is available yet for this article.
January 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29226385/methods-for-meta-analysis-of-multiple-traits-using-gwas-summary-statistics
#8
Debashree Ray, Michael Boehnke
Genome-wide association studies (GWAS) for complex diseases have focused primarily on single-trait analyses for disease status and disease-related quantitative traits. For example, GWAS on risk factors for coronary artery disease analyze genetic associations of plasma lipids such as total cholesterol, LDL-cholesterol, HDL-cholesterol, and triglycerides (TGs) separately. However, traits are often correlated and a joint analysis may yield increased statistical power for association over multiple univariate analyses...
December 10, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/29225345/common-variants-at-2q11-2-8q21-3-and-11q13-2-are-associated-with-major-mood-disorders
#9
Xiao Xiao, Lu Wang, Chuang Wang, Ti-Fei Yuan, Dongsheng Zhou, Fanfan Zheng, Lingyi Li, Maria Grigoroiu-Serbanescu, Masashi Ikeda, Nakao Iwata, Atsushi Takahashi, Yoichiro Kamatani, Michiaki Kubo, Martin Preisig, Zoltán Kutalik, Enrique Castelao, Giorgio Pistis, Najaf Amin, Cornelia M van Duijn, Andreas J Forstner, Jana Strohmaier, Julian Hecker, Thomas G Schulze, Bertram Müller-Myhsok, Andreas Reif, Philip B Mitchell, Nicholas G Martin, Peter R Schofield, Sven Cichon, Markus M Nöthen, Hong Chang, Xiong-Jian Luo, Yiru Fang, Yong-Gang Yao, Chen Zhang, Marcella Rietschel, Ming Li
Bipolar disorder (BPD) and major depressive disorder (MDD) are primary major mood disorders. Recent studies suggest that they share certain psychopathological features and common risk genes, but unraveling the full genetic architecture underlying the risk of major mood disorders remains an important scientific task. The public genome-wide association study (GWAS) data sets offer the opportunity to examine this topic by utilizing large amounts of combined genetic data, which should ultimately allow a better understanding of the onset and development of these illnesses...
December 11, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/29225335/genetic-architecture-the-shape-of-the-genetic-contribution-to-human-traits-and-disease
#10
REVIEW
Nicholas J Timpson, Celia M T Greenwood, Nicole Soranzo, Daniel J Lawson, J Brent Richards
Genetic architecture describes the characteristics of genetic variation that are responsible for heritable phenotypic variability. It depends on the number of genetic variants affecting a trait, their frequencies in the population, the magnitude of their effects and their interactions with each other and the environment. Defining the genetic architecture of a complex trait or disease is central to the scientific and clinical goals of human genetics, which are to understand disease aetiology and aid in disease screening, diagnosis, prognosis and therapy...
December 11, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29224884/a-genome-wide-association-study-for-left-sided-displacement-of-the-abomasum-using-a-high-density-single-nucleotide-polymorphism-array
#11
S Lehner, I Zerbin, K Doll, J Rehage, O Distl
Left-sided displacement of the abomasum (LDA) is a frequent disease in dairy cattle causing significant financial losses for dairy farmers. Heritability (h2) of this complex disease was estimated at up to 0.5 in German Holstein (GH) cattle. Using the Bovine High Density BeadChip (Illumina Inc., San Diego, CA) comprising 588,753 single nucleotide polymorphisms (SNP) after quality control for 126 LDA cases and 280 population-based controls, we used a mixed linear model analysis in a genome-wide association study (GWAS)...
December 7, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29224151/a-guide-to-illumina-beadchip-data-analysis
#12
Michael C Wu, Pei-Fen Kuan
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224150/bisulphite-sequencing-of-chromatin-immunoprecipitated-dna-bischip-seq
#13
Clare Stirzaker, Jenny Z Song, Aaron L Statham, Susan J Clark
Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224145/methyl-cpg-binding-domain-sequencing-mbd-seq
#14
Karolina A Aberg, Robin F Chan, Linying Xie, Andrey A Shabalin, Edwin J C G van den Oord
Detailed biological knowledge about the potential importance of the methylome is typically lacking for common diseases. Therefore, methylome-wide association studies (MWAS) are critical to detect disease relevant methylation sites. Methyl-CpG-binding domain sequencing (MBD-seq) offers potential advantages compared to antibody-based enrichment, but performance depends critically on using an optimal protocol. Using an optimized protocol, MBD-seq can approximate the sensitivity/specificity obtained with whole-genome bisulfite sequencing, but at a fraction of the costs and time to complete the project...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224136/a-summary-of-the-biological-processes-disease-associated-changes-and-clinical-applications-of-dna-methylation
#15
Gitte Brinch Andersen, Jörg Tost
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223971/keeping-pace-with-the-red-queen-identifying-the-genetic-basis-of-susceptibility-to-infectious-disease
#16
Ailene MacPherson, Sarah P Otto, Scott L Nuismer
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations...
December 9, 2017: Genetics
https://www.readbyqxmd.com/read/29223691/genome-wide-association-analysis-of-ear-rot-resistance-caused-by-fusarium-verticillioides-in-maize
#17
Guilherme de Jong, Andrezza Kellen Alves Pamplona, Renzo Garcia Von Pinho, Marcio Balestre
The identification of causal regions associated with resistance to Fusarium verticillioides can be useful to understand resistance mechanisms and further be used in breeding programs. In this study, a genome-wide association study (GWAS) was conducted to identify candidate markers associated with resistance to the ear rot caused by the fungus F. verticillioides. A total of 242 maize inbred lines were genotyped with 23,153 DArT-seq markers. A total of 12 DArTs were associated with ear rot resistance. Some DArTs were localized close to genes with functions directly related to ear rot resistance, such as a gene responsible for the innate immune response that belongs to the class of NBS-LRR receptors...
December 6, 2017: Genomics
https://www.readbyqxmd.com/read/29222496/genome-wide-and-gene-based-association-mapping-for-rice-eating-and-cooking-characteristics-and-protein-content
#18
Xiaoqian Wang, Yunlong Pang, Jian Zhang, Zhichao Wu, Kai Chen, Jauhar Ali, Guoyou Ye, Jianlong Xu, Zhikang Li
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221444/genome-wide-association-study-of-coronary-artery-calcified-atherosclerotic-plaque-in-african-americans-with-type-2-diabetes
#19
Jasmin Divers, Nicholette D Palmer, Carl D Langefeld, W Mark Brown, Lingyi Lu, Pamela J Hicks, S Carrie Smith, Jianzhao Xu, James G Terry, Thomas C Register, Lynne E Wagenknecht, John S Parks, Lijun Ma, Gary C Chan, Sarah G Buxbaum, Adolfo Correa, Solomon Musani, James G Wilson, Herman A Taylor, Donald W Bowden, John Jeffrey Carr, Barry I Freedman
BACKGROUND: Coronary artery calcified atherosclerotic plaque (CAC) predicts cardiovascular disease (CVD). Despite exposure to more severe conventional CVD risk factors, African Americans (AAs) are less likely to develop CAC, and when they do, have markedly lower levels than European Americans. Genetic factors likely contribute to the observed ethnic differences. To identify genes associated with CAC in AAs with type 2 diabetes (T2D), a genome-wide association study (GWAS) was performed using the Illumina 5 M chip in 691 African American-Diabetes Heart Study participants (AA-DHS), with replication in 205 Jackson Heart Study (JHS) participants with T2D...
December 8, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29220677/a-powerful-approach-to-estimating-annotation-stratified-genetic-covariance-via-gwas-summary-statistics
#20
Qiongshi Lu, Boyang Li, Derek Ou, Margret Erlendsdottir, Ryan L Powles, Tony Jiang, Yiming Hu, David Chang, Chentian Jin, Wei Dai, Qidu He, Zefeng Liu, Shubhabrata Mukherjee, Paul K Crane, Hongyu Zhao
Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics...
December 7, 2017: American Journal of Human Genetics
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